[gmx-users] how to use the trjconv -sep and -skip to get the individual file

Francesco fracarb at myopera.com
Fri Apr 19 17:44:01 CEST 2013

if you only want the pdb file at a specific moment you can use -dump
trjconv -f traj.xtc -s file.tpr -o pdb_at_time.pdb -dump 10

the "pdb_at_time.pdb" file will be the structure at 10 ps.

You can then write a script to go through all your simulation.



On Fri, 19 Apr 2013, at 12:16 PM, aixintiankong wrote:
> Dear,
>       I have made a 10ns prodution MD, The set  dt=0.002,nstxtcout   =
>       500 in mdp file.   I have made 10ns prodution MD, I want to extract
>       frames from the molecular dynamics simulations at regular intervals
>       of 10ps and keep the file as individual pdb file   i want to use
>       the follow command ,
>            trjconv -s topol.tpr -f traj.xtc -skip (number) -o conf.pdb
>            -sep
> but i don't now how to set the number of skip,please help me and tell me
> what the skip mean
> thank you !
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

  fracarb at myopera.com

More information about the gromacs.org_gmx-users mailing list